Forgiveness
by Lorr
Summary: These are two missing scenes at the end of Instinct, just before the last scene. Complete.


**Title:** Forgiveness

**Author:** Lorr

**Genre/Rating:** General – Missing Scenes

**Character:** Weir, Sheppard, Beckett, McKay, Teyla, Ronon

**Disclaimer:** The characters and universe do not belong to me. I'm just visiting.

**Spoilers:** None that I know of.

**Background:** This is at the end of Conversion, right before the last scene. I am getting my fix in by writing these while I working on some details of a proper story. I hope you enjoy.

Elizabeth Weir looked anxiously from Dr. Beckett to John Sheppard. She was sitting in the infirmary, next to Sheppard's bed. The head of the bed was raised about forty-five degrees. Beckett was adjusting the flow rate in Sheppard's IV.

"Carson, you said the transformation isn't anywhere near complete. Are you sure it's okay to bring him out of the coma?"

"No, but I can't keep him like this any longer. It's been ten days since we started the treatment. Besides, I've asked Ronon and Teyla to be here. Ronon is bringing his pistol. Don't worry, he'll set it on stun." Beckett scanned the monitors and checked the nutrient liquid being given to the sleeping man through a nasal feeding tube. "Elizabeth, John will more likely be weak as a kitten. His system wasn't even able to metabolize this nutritional liquid until yesterday. He was on saline only for nearly two weeks. And, the massive changes his body's gone through have drained his reserves."

"Right now, I'm more worried about his mind, Carson." She held Sheppard's left hand but could not lift it. His wrists and ankles were secured to the bed by snug restraints. "Were we in time?"

"Honestly, I don't know. We'll have to wait and see." Beckett picked up the chart and entered some figures and notes.

Ronon, Teyla and McKay entered the infirmary and hovered at the edge of the screens that blocked the bed from view of the rest of the room. They closely studied Sheppard then Beckett and Elizabeth, looking for any indication of the Colonel's condition. Ronon silently slid his gun from its holster.

"Well, Carson, it's about time." McKay said with relief and apprehension in his voice at the same time.

"Rodney, the stem cell therapy had a lot of damage to undo and is still reconstructing his DNA. It's actually going better than I thought." Beckett glared at McKay before checking the monitors again and listening to Sheppard's heart and lungs with his stethoscope. "Besides that, the whole process is probably quite painful. I didn't want to wake him up just to have to pump him full of narcotics. He's been through enough already."

McKay looked hurt. "That's not what I meant. I'm just happy it's happening at all."

The conversion from human to the uncontrollable creature that had emerged from the cave took nearly a week. The change back to human, with fully human DNA was taking longer. They could see that at least Sheppard's right arm and hand still bore visible signs of the creature. They knew his internal organs were not quite right yet either, and they were all worried about his mind.

"We know, Rodney. It's been a long wait for everyone." Elizabeth glanced at him and up at the Doctor.

Beckett nodded tight-lipped at McKay before gently lifting the lid of the Colonel's right eye and flicking his flashlight across it. The others leaned forward to see whether it was Sheppard's own grey iris or the animal-like yellow with an unnerving vertical pupil. They all exhaled in relief at the glimpse of a very human eye then stiffened as Sheppard turned his head a fraction to avoid the light. A moment later, both eyes blinked wide, but closed again.

"John?" Elizabeth squeezed the hand she still held and stood up.

Sheppard's breathing deepened and his eyes opened. He frowned and looked around in confusion.

"Colonel?" Beckett put his hand on Sheppard's shoulder. "Do you know where you are?"

"'Firmary." Sheppard's voice was hoarse. He took a moment to focus on Beckett then turned his head to look at Elizabeth. He cleared his throat and swallowed hard. "'V'ryone okay?"

"Yes, John, everyone is fine." Elizabeth's voice caught as she smiled at him. She quickly brushed her cheek as the rest beamed at each other. She looked down at the restraints holding the Colonel's wrists. "Carson? Can we take these off?"

"Aye, I think so." Beckett shot a warning glance at Ronon before he nodded and he began to take off the straps on the right side. Elizabeth removed those on the left side.

In seconds, the restraints were tossed on a nearby bed. Sheppard lifted his unsteady hands a few inches to look at them. He saw the left appeared normal, but the right was not quite completely human. After studying them for a moment, he let them drop back to the bed. When he tried to speak, his voice was nothing more than a whisper.

"Water." Sheppard licked dry lips. Beckett raised the bed head a little more and held the glass for his patient to drink. After several slow swallows, Sheppard released the straw and the Doctor put the glass back on the table. "Thanks. How'm I doing?"

Beckett touched Sheppard's right hand. "You're doing fine, laddie. This'll be gone before you know it."

Ronon quietly holstered his weapon. His whole body visibly relaxed, as did Teyla's. McKay grabbed the end of the bed, visibly relieved.

"DNA?"

""It's getting there. The stem cell therapy is doing better than I hoped." Beckett watched his patient closely. "How are you feeling? Are you in any pain?"

"Not much." Sheppard took a deep breath and closed his eyes for a moment. "Aches a little, like the flu."

"Liar." Beckett picked up a syringe and vial from the bedside table. He injected a small amount of the drug into the IV line. "This will help you sleep."

"Already?" Sheppard grimaced at the Doctor.

"A little more won't hurt, John." Beckett spoke softly and patted Sheppard's arm.

"Long've I been 'ere?" As the drug took hold, the Colonel's voice began to slur.

McKay spoke up. "It's been ten days since you went to the cave.

"Ten? 'S record fer me." Sheppard struggled to stay awake for a little longer. His eyes finally closed.

"I think he's going to be okay." Beckett sighed as he turned to the others. "He'll be asleep for a couple of hours."

Elizabeth stopped at the pillar in the middle of the room. Beckett was standing with his back to her, blocking Sheppard's view of the infirmary door. The two were talking. She froze, unable to decide whether she should try to sneak back out or continue in and interrupt.

"Doc, it wasn't your fault. Let it go." The Colonel's voice was much stronger, and sounding a mite exasperated. The Doctor brought him out of the medically induced coma two days ago and his progress had been good.

"I appreciate your saying that, John, but it doesn't relieve me of the responsibility." Beckett was still guilt-stricken over the fact that Ellia had taken the retrovirus and infected Sheppard with it, coming all too close to turning him into a...a…no-one knew what to call the creature.

Sheppard's voice softened now, and dropped to just above a whisper. "Carson, you were only trying to do something good. You had no control over what happened."

At that moment, the Doctor moved just enough for Sheppard to see Elizabeth. He smiled broadly, prompting Beckett to turn.

"Elizabeth!"

"You seem to be feeling a lot better." She smiled as she approached the bed. "Am I interrupting something?"

"No, no." Beckett shook his head.

"How is the patient today?" Elizabeth asked. She was happy to see the monitors, IV and feeding tube were gone. Beckett must be confident that he was near normal internally. That meant Sheppard was able to eat real food again.

Before the Colonel could answer, Beckett spoke. "Well enough to kick out of here in two or three days. It'll be nice to have my infirmary back."

Sheppard grinned. "You could let me go to my quarters right now."

"No." The Doctor turned to Elizabeth. "I'll leave you to amuse him. I have some paperwork to attend to."

As Beckett left, she sat on the chair next to the bed and smiled warmly at Sheppard. "How are you?"

"Fine. Doc says I'm almost a hundred percent me again." He held up his right arm to show her that his hand was fully human looking. The abnormal area of his arm was much smaller. "He says this is going to take some time, but it will go away."

"So, he's going to spring you soon?"

"Yeah, bless his heart." He grinned again.

Elizabeth tapped the data pad leaning against his leg. "What's this?"

"Oh, I was just looking over the changes Col. Caldwell made while I was…ah…out of the picture." Sheppard raised a conspiratorial eyebrow. "Just between you and me, if I were the paranoid type, I'd think he was after my job."

She looked guilty. "I'm sorry, John. I asked him to look after things until you were better. But, you are the military commander of Atlantis. You do whatever you think best."

"Don't worry about it. He actually did me a favor." He moved the pad to the bedside table and dismissed it with a wave. "Hell, Elizabeth, I'm a pilot, not an administrator. I don't agree with some of the assignments, but, on the whole…"

"He'll be happy to hear that, I'm sure." She said without really believing it.

"I'm sure." He agreed then looked at her with an 'are you kidding me' expression. They both chuckled for a moment.

Suddenly, Sheppard turned serious and studied her closely. He lowered his voice. "Elizabeth?"

His obvious concern alarmed her. "What's wrong?"

Sheppard chewed on his lower lip for a moment. "It's taken me long enough, but I think I've pieced together most of what happened after Ellia infected me.

"Oh!"

Elizabeth's hand went to her throat before she could stop herself. Sheppard's reaction was just as quick and unstoppable. It was as if he had been hit hard. He closed his eyes tight and turned his head away.

"John." She touched his arm.

He turned back and whispered. "I almost killed you."

"You didn't. I'm fine." She had dreaded that he would remember that moment.

"I am sorry." Sheppard searched her neck then her face for any signs of injury, physical or emotional. He reached out to touch her, but quickly drew his hand back. "Did I hurt you?"

"No, no. There wasn't even a bruise." Elizabeth grasped his hand and smiled reassuringly. "Honestly. You only startled me."

She could see real fear and pain in his eyes. "But I could have. Elizabeth, there was almost none of me left."

"There was enough. John, I trust you." Now she reached out and put her hand on his cheek.

"That day, at that time, you shouldn't have. I nearly cost both of us everything."

Elizabeth was taken aback for a moment then she wrapped both hands around his and held it tight.

"John, you are in no way responsible for what happened. You should take the advice you gave Carson. It wasn't your fault. Let it go."


End file.
